Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-07-31 12:06:52 -0400 (Sat, 31 Jul 2021).

CHECK results for RCy3 on merida1

To the developers/maintainers of the RCy3 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCy3.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1505/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.13.3  (landing page)
Alex Pico
Snapshot Date: 2021-07-30 14:50:06 -0400 (Fri, 30 Jul 2021)
URL: https://git.bioconductor.org/packages/RCy3
Branch: master
Last Commit: 36f52f2
Last Changed Date: 2021-06-15 21:29:56 -0400 (Tue, 15 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RCy3
Version: 2.13.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCy3_2.13.3.tar.gz
StartedAt: 2021-07-31 05:59:35 -0400 (Sat, 31 Jul 2021)
EndedAt: 2021-07-31 06:01:56 -0400 (Sat, 31 Jul 2021)
EllapsedTime: 140.5 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCy3_2.13.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/RCy3.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.13.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RCy3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.edgeNameToEdgeSUID: no visible binding for global variable ‘SUID’
.nodeNameToNodeSUID: no visible binding for global variable ‘SUID’
commandsGET: no visible binding for global variable ‘requester’
commandsHelp: no visible binding for global variable ‘requester’
commandsPOST: no visible binding for global variable ‘requester’
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
cyrestDELETE: no visible binding for global variable ‘requester’
cyrestGET: no visible binding for global variable ‘requester’
cyrestPOST: no visible binding for global variable ‘requester’
cyrestPUT: no visible binding for global variable ‘requester’
paletteColorRandom: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  SUID requester rgb
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘RCy3’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCy3)

Tests output

RCy3.Rcheck/tests/runTests.Rout


R version 4.1.0 RC (2021-05-16 r80304) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # tests disabled as the Bioconductor build system no longer supports interactive sessions
> #require(RCy3) || stop("unable to load RCy3")
> #BiocGenerics:::testPackage('RCy3')
> 
> proc.time()
   user  system elapsed 
  0.225   0.060   0.260 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

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checkRunningRemote000
clearEdgeBends0.0000.0000.001
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clearNetworkZoomBypass000
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection000
cloneNetwork000
closeSession0.0000.0010.000
collapseGroup000
commandEcho000
commandOpenDialog000
commandPause0.0000.0000.001
commandQuit0.0000.0010.000
commandRunFile0.0000.0000.001
commandSleep000
commandsAPI000
commandsGET0.0000.0000.001
commandsHelp000
commandsPOST000
commandsRun0.0000.0000.001
copyVisualStyle000
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createCompositeFilter0.0000.0010.000
createDegreeFilter0.0000.0000.001
createGraphFromNetwork0.0000.0000.001
createGroup0.0010.0000.000
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromDataFrames000
createNetworkFromGraph0.0000.0000.001
createNetworkFromIgraph0.0000.0010.000
createSubnetwork000
createVisualStyle000
cybrowserClose000
cybrowserDialog0.0010.0000.001
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion0.0010.0000.000
cyrestAPI000
cyrestDELETE000
cyrestGET000
cyrestPOST000
cyrestPUT0.0000.0000.001
cytoscapeApiVersions000
cytoscapeFreeMemory0.0000.0000.001
cytoscapeMemoryStatus0.0000.0000.001
cytoscapeNumberOfCores0.0000.0000.001
cytoscapePing0.0000.0000.001
cytoscapeVersionInfo000
deleteAllNetworks0.0000.0010.000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup000
deleteNetwork000
deleteSelectedEdges000
deleteSelectedNodes0.0000.0010.001
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn0.0000.0000.001
deleteVisualStyle0.0000.0010.000
diffusionAdvanced0.0010.0000.000
diffusionBasic000
disableApp000
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doRequestRemote000
doSetSandbox000
dockPanel000
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dot-getRequester0.0000.0000.001
enableApp000
expandGroup0.0010.0000.001
exportFilters0.0010.0000.000
exportImage000
exportNetwork000
exportNetworkToNDEx0.0000.0000.001
exportVisualStyles000
findRemoteCytoscape000
fitContent0.0000.0010.000
floatPanel000
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getDefaultSandbox000
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getEdgeSelectionColorDefault0.0000.0000.001
getEdgeTargetArrowShape0.0000.0000.001
getFilterList0.0000.0000.001
getFirstNeighbors0.0000.0010.000
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getInstalledApps000
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getNetworkCenter0.0000.0000.001
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount000
getNodeHeight000
getNodePosition0.0000.0000.001
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getNodeSelectionColorDefault0.0000.0000.001
getNodeShapes0.0000.0010.000
getNodeSize000
getNodeWidth000
getNotebookIsRunning0.0010.0010.000
getSandboxReinitialize000
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getSelectedEdges0.0010.0000.001
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hideNodes0.0010.0010.001
hidePanel000
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importVisualStyles0.0000.0010.000
installApp000
invertEdgeSelection0.0000.0000.001
invertNodeSelection0.0000.0010.000
layoutCopycat0.0000.0000.001
layoutNetwork0.0000.0010.001
listGroups000
lockNodeDimensions000
makeSimpleGraph0.1020.0010.104
makeSimpleIgraph0.0120.0010.013
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matchArrowColorToEdge0.0000.0000.001
mergeNetworks0.0000.0010.000
openAppStore000
openSession000
paletteColorBrewerAccent0.0050.0000.006
paletteColorBrewerBlues000
paletteColorBrewerBrBG0.0010.0000.000
paletteColorBrewerBuGn000
paletteColorBrewerBuPu000
paletteColorBrewerDark20.0010.0000.001
paletteColorBrewerGnBu0.0000.0000.001
paletteColorBrewerGreens0.0000.0000.001
paletteColorBrewerGreys0.0010.0010.000
paletteColorBrewerOrRd0.0000.0000.001
paletteColorBrewerOranges0.0010.0000.000
paletteColorBrewerPRGn0.0010.0000.000
paletteColorBrewerPaired000
paletteColorBrewerPastel1000
paletteColorBrewerPastel20.0010.0000.001
paletteColorBrewerPiYG0.0000.0010.001
paletteColorBrewerPuBu0.0000.0000.001
paletteColorBrewerPuBuGn0.0000.0000.001
paletteColorBrewerPuOr0.0000.0010.000
paletteColorBrewerPuRd000
paletteColorBrewerPurples0.0000.0000.001
paletteColorBrewerRdBu0.0000.0010.001
paletteColorBrewerRdPu0.0000.0000.001
paletteColorBrewerRdYlBu000
paletteColorBrewerReds000
paletteColorBrewerSet10.0000.0010.001
paletteColorBrewerSet20.0000.0010.001
paletteColorBrewerSet3000
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paletteColorBrewerYlOrRd000
paletteColorRandom0.0010.0000.000
removeNodeCustomGraphics000
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runningRemoteCheck0.0000.0000.001
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setEdgeLabelOpacityBypass000
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setEdgeLabelOpacityMapping000
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setEdgePropertyBypass0.0000.0010.001
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